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This chapter provides a focused examination of spatio-temporal analysis using multilayer networks in which each layer represents the instantiation of a spatial network at a particular time of observation. The nodes in all layers may be the same with the only differences being of edges among layers (a multiplex network) or the nodes may change or move between layers and times. Multilayer characteristics such as versatility (multilayer centrality) and spectral properties are introduced. Several examples are described and reviewed as model studies for future ecological applications.
Sets of points can be analysed from their positions in space and line segments can be studied separately for their own spatial arrangements and relationships. Combining points and lines as the nodes and edges of a spatial graph provides a flexible and powerful approach to spatial analysis. Such graphs and their network versions are studied by Graph Theory, a branch of mathematics that quantifies their properties, with or without additional features such as labels, weights and functions associated with the nodes and edges. Some relevant graph theory terms are introduced, including connectivity, connectedness, modularity and centrality. Networks are graphs with additional features, usually representing an observed system of interest, whether aspatial like a food web or spatial like a metacommunity. Key concepts for the latter example are connectivity, migration and network flow.
The Amazon comprises the most biodiverse region in the world, but, despite being highly threatened by human-induced environmental changes, little is known about how those changes influence the remaining forest’s extent and configuration in Brazil’s arc of deforestation. We analysed the spatial and temporal dynamics and the configuration of forest cover in Brazil’s state of Rondônia over 34 years. We calculated seven landscape metrics based on freely available satellite imagery to understand the habitat transformations. Overall, natural vegetation cover declined from 90.9% to 62.7% between 1986 and 2020, and fragmentation greatly increased, generating 78 000 forest fragments and 100 000 fragments of ‘natural vegetation’, which also includes forest. We found that c. 50% of the vegetation is within c. 1 km of the nearest forest edge, and the mean isolation between fragments is c. 2.5 km. Most natural vegetation and forest vegetation layers outside protected areas (PAs; Brazil’s ‘conservation units’) and Indigenous territories (ITs) are >10 km from the nearest PA or IT. This reduction of natural vegetation in Rondônia is posing major threats to the survival of species and is undermining the dynamics of ecosystems. Measures to control deforestation and avoid the reduction of large remnants are urgently needed.
Parkinson’s disease (PD) has become the second most prominent neurogenerative disorder relating to aging individuals. PD involves the loss of neurons containing dopamine in the midbrain and leads to a number of motor issues as well as non-motor complications such as cognitive and psychological abnormalities. The default mode network (DMN) is a complex brain network primarily active during rest and serves multiple roles relating to memory, self-referential processing, social cognition and consciousness and awareness. Multiple brain regions are involved in the DMN such as the medial prefrontal cortex (mPFC), the posterior cingulate cortex (PCC), the inferior parietal lobule, the precuneus and the lateral temporal cortex. Normal DMN connectivity is vital to preserving consciousness and self-awareness. Neurological pathologies such as PD disrupt DMN connectivity, leading to complex issues. Functional MRI (fMRI) is a neuroimaging modality used to observe brain activity through measuring blood flow differences as it relates to brain activity. DMN connectivity experiments using fMRI find that individuals with PD exhibit impaired DMN connectivity in specific regions including the PCC, mPFC and the precuneus. Individuals with greater PD motor symptoms have also been found to suffer larger alterations in DMN connections anatomically within the frontal lobe and PCC. While fMRI has been utilized as a tool to explore the relationship between PD patients and DMN connectivity, future research should look to develop a better understanding of the specific mechanisms of action that drive this link between DMN abnormality and PD severity.
Hillslopes may be regarded as conveyor belts transferring water and sediment and nutrients to other parts of the geomorphic system. This chapter examines the mechanisms of, and the factors controlling, how far and how fast water, sediment and nutrients move along this conveyor belt, discussing water movement in and on hillslopes, fluid-gravity and sediment-gravity movement of sediment and nutrient movement. Hillslope processes do not operate in isolation, and the interaction, of connectivity among processes is also important. This interaction is particularly significant when assessing the importance of connectivity to understanding hillslopes within the context of landscape evolution. A full description of the connectivity of hillslope processes will require combined knowledge of both the magnitude–connectivity relationship, the probability distribution of event magnitudes and, to explain specific cases of functional connectivity, the actual sequence of events. In recent years there has been a growing recognition of the importance of connectivity in understanding the effects of hillslope processes. At best, however, that understanding remains patchy and incomplete.
This chapter discusses what is meant by connectivity in fluvial systems and how the connectivity approach differs from preceding research, the way in which it increases understanding of fluvial processes, and how knowledge of mechanisms and dynamics of processes fits into this framework. The focus is on longitudinal connectivity through river systems, mainly in large catchments and river channels and much of the attention is on sediment connectivity. The application of connectivity indices and graph theory are exemplified and the patterns, distributions and controls produced by connectivity analysis are demonstrated. Lateral connectivity is important in relation to the link of channels to floodplains and in maintaining functioning of wetlands. Recent developments of techniques and models have allowed additional factors to be incorporated and controls on connectivity of fluvial processes to be identified. The use of connectivity analysis as a framework is highly beneficial in management of fluvial systems and facilitates targeting of hotspots of sediment accumulation or depletion.
Farming has modified the natural dynamic of soil erosion/redistribution in significant parts of landscapes, triggering high rates of soil loss and accelerating sediment connectivity. This chapter provides a review of sediment connectivity in grassland, herbaceous and woody crops from knowledge to management. The first section explores the extension of farmland at a global scale and the process of agricultural land expansion. Regarding herbaceous crops, the second section highlights the importance of cropping intensity (one or two crops per year), water supply (rainfed or irrigated), and crop rotation on the sediment-connectivity magnitude. In the section of woody crops, studies done in vineyards, olive groves and citrus orchards describe the processes of sediment connectivity with and without soil conservation practices (e.g., cover crops). The section of sediment connectivity in grasslands includes examples in alpine hillsides, valley bottom and lakes, emphasizing their role as sediment-trapping features. The last section deals with sediment dis-connectivity in farmland due to soil erosion control practices and governmental programs, with examples from Europe and China.
While recent aDNA and other scientific analysis has served to underline the recurrent role of migration in the process of Neolithisation right across Europe, there remains plenty of scope for better integration of archaeogenetic and archaeological interpretations and for detailed narratives of local and regional trajectories. This paper focuses on relations between Britain and Ireland in the early Neolithic, in the first part of the 4th millennium cal BC. I argue that direct connections between Britain and Ireland have been overlooked and underplayed — hidden in plain sight — in the search for perceived common sources in continental Europe. I advance four propositions for debate: that the first Neolithic people in Ireland came mainly from Britain, perhaps from several parts of western Britain; that subsequent connections, long described but curiously not much further interpreted, constitute an intense set of interactions; that such links were probably spread over time through the early Neolithic, coming thick and fast near the beginning and perhaps even intensifying with time; and that such relations were maintained and intensified because of the concentrated circumstances of beginnings. The latter arguably contrast with those of the relationship between the Continent and southern Britain. The maintenance of connections was political, because a remembered past was actively used; lineage founders, concentrated lineages and other emergent social groupings may have developed through time as part of such a process.
This study employs neutron activation analysis (NAA) to examine pottery from Middle Bronze Age (MBA) (c. 2200–1700 bc) Mitrou in East Lokris, central Greece. The analysis of 112 samples from all ceramic phases reveals complex patterns of production and exchange at multiple scales. Limited production of tablewares is evident within the immediate coastscape, contrasting sharply with abundant imports of tableware from other communities (most prominently, central Euboea and Boeotia), revealing a highly interconnected central Greek world. The NAA results also reinforce previous petrographic analysis, emphasizing connections with the broader regional maritime sphere, including the Cyclades, Aegina, Crete, and the south-eastern Aegean. The results challenge previous perceptions of the central Greek MBA as isolated, provide new insights into MBA connectivity, and highlight the need for further analytical work at other central Greek sites.
Searching for the Neolithic along the Vardar-Morava River corridor revealed several new sites in a previously underexplored region. Multidisciplinary investigations at Svinjarička Čuka identified Neolithic and Bronze Age occupation. Highlights presented here demonstrate the potential of this new key site for enriching our understanding of the prehistory of the Balkans.
The rising incidence of neurodegenerative diseases in an ageing global population has shifted research focus towards modifiable risk factors, such as diet. Despite potential links between dietary patterns and brain health, inconsistencies in neuroimaging outcomes underscore a gap in understanding how diet impacts brain ageing. This study explores the relationship between three dietary patterns – Mediterranean, Dietary Approaches to Stop Hypertension (DASH) and Mediterranean-DASH Intervention for Neurodegenerative Delay – and cognitive outcomes as well as brain connectivity. The study aimed to assess the association of these diets with brain structure and cognitive function, involving a middle-aged healthy group and an older cohort with subjective cognitive decline. The study included cognitive assessments and diffusion-weighted MRI data to analyse white matter microstructural integrity. Participants comprised fifty-five older individuals with subjective cognitive decline (54·5 % female, mean age = 64) and fifty-two healthy middle-aged individuals (48·1 % female, mean age = 53). Age inversely correlated with certain cognitive functions and global brain metrics, across both cohorts. Adherence to the Mediterranean, DASH and Mediterranean-DASH Intervention for Neurodegenerative Delay diets showed no significant cognitive or global brain metric improvements after adjusting for covariates (age, education, BMI). Network-based statistics analysis revealed differences in brain subnetworks based on DASH diet adherence levels in the subjective cognitive decline cohort. In the healthy cohort, lower white matter connectivity was associated with reduced adherence to Mediterranean-DASH Intervention for Neurodegenerative Delay and DASH diets. Ultimately, the study found no strong evidence connecting dietary patterns to cognitive or brain connectivity outcomes. Future research should focus on longitudinal studies and refine dietary assessments.
We consider the count of subgraphs with an arbitrary configuration of endpoints in the random-connection model based on a Poisson point process on ${\mathord{\mathbb R}}^d$. We present combinatorial expressions for the computation of the cumulants and moments of all orders of such subgraph counts, which allow us to estimate the growth of cumulants as the intensity of the underlying Poisson point process goes to infinity. As a consequence, we obtain a central limit theorem with explicit convergence rates under the Kolmogorov distance and connectivity bounds. Numerical examples are presented using a computer code in SageMath for the closed-form computation of cumulants of any order, for any type of connected subgraph, and for any configuration of endpoints in any dimension $d{\geq} 1$. In particular, graph connectivity estimates, Gram–Charlier expansions for density estimation, and correlation estimates for joint subgraph counting are obtained.
Working memory deficit, a key feature of schizophrenia, is a heritable trait shared with unaffected siblings. It can be attributed to dysregulation in transitions from one brain state to another.
Aims
Using network control theory, we evaluate if defective brain state transitions underlie working memory deficits in schizophrenia.
Method
We examined average and modal controllability of the brain's functional connectome in 161 patients with schizophrenia, 37 unaffected siblings and 96 healthy controls during a two-back task. We use one-way analysis of variance to detect the regions with group differences, and correlated aberrant controllability to task performance and clinical characteristics. Regions affected in both unaffected siblings and patients were selected for gene and functional annotation analysis.
Results
Both average and modal controllability during the two-back task are reduced in patients compared to healthy controls and siblings, indicating a disruption in both proximal and distal state transitions. Among patients, reduced average controllability was prominent in auditory, visual and sensorimotor networks. Reduced modal controllability was prominent in default mode, frontoparietal and salience networks. Lower modal controllability in the affected networks correlated with worse task performance and higher antipsychotic dose in schizophrenia (uncorrected). Both siblings and patients had reduced average controllability in the paracentral lobule and Rolandic operculum. Subsequent out-of-sample gene analysis revealed that these two regions had preferential expression of genes relevant to bioenergetic pathways (calmodulin binding and insulin secretion).
Conclusions
Aberrant control of brain state transitions during task execution marks working memory deficits in patients and their siblings.
There is increasing use of functional imaging data to understand the macro-connectome of the human brain. Of particular interest is the structure and function of intrinsic networks (regions exhibiting temporally coherent activity both at rest and while a task is being performed), which account for a significant portion of the variance in functional MRI data. While networks are typically estimated based on the temporal similarity between regions (based on temporal correlation, clustering methods, or independent component analysis [ICA]), some recent work has suggested that these intrinsic networks can be extracted from the inter-subject covariation among highly distilled features, such as amplitude maps reflecting regions modulated by a task or even coordinates extracted from large meta analytic studies. In this paper our goal was to explicitly compare the networks obtained from a first-level ICA (ICA on the spatio-temporal functional magnetic resonance imaging (fMRI) data) to those from a second-level ICA (i.e., ICA on computed features rather than on the first-level fMRI data). Convergent results from simulations, task-fMRI data, and rest-fMRI data show that the second-level analysis is slightly noisier than the first-level analysis but yields strikingly similar patterns of intrinsic networks (spatial correlations as high as 0.85 for task data and 0.65 for rest data, well above the empirical null) and also preserves the relationship of these networks with other variables such as age (for example, default mode network regions tended to show decreased low frequency power for first-level analyses and decreased loading parameters for second-level analyses). In addition, the best-estimated second-level results are those which are the most strongly reflected in the input feature. In summary, the use of feature-based ICA appears to be a valid tool for extracting intrinsic networks. We believe it will become a useful and important approach in the study of the macro-connectome, particularly in the context of data fusion.
Major psychiatric disorders (MPDs) are delineated by distinct clinical features. However, overlapping symptoms and transdiagnostic effectiveness of medications have challenged the traditional diagnostic categorisation. We investigate if there are shared and illness-specific disruptions in the regional functional efficiency (RFE) of the brain across these disorders.
Methods
We included 364 participants (118 schizophrenia [SCZ], 80 bipolar disorder [BD], 91 major depressive disorder [MDD], and 75 healthy controls [HCs]). Resting-state fMRI was used to caclulate the RFE based on the static amplitude of low-frequency fluctuation, regional homogeneity, and degree centrality and corresponding dynamic measures indicating variability over time. We used principal component analysis to obtain static and dynamic RFE values. We conducted functional and genetic annotation and enrichment analysis based on abnormal RFE profiles.
Results
SCZ showed higher static RFE in the cortico-striatal regions and excessive variability in the cortico-limbic regions. SCZ and MDD shared lower static RFE with higher dynamic RFE in sensorimotor regions than BD and HCs. We observed association between static RFE abnormalities with reward and sensorimotor functions and dynamic RFE abnormalities with sensorimotor functions. Differential spatial expression of genes related to glutamatergic synapse and calcium/cAMP signaling was more likely in the regions with aberrant RFE.
Conclusions
SCZ shares more regions with disrupted functional integrity, especially in sensorimotor regions, with MDD rather than BD. The neural patterns of these transdiagnostic changes appear to be potentially driven by gene expression variations relating to glutamatergic synapses and calcium/cAMP signaling. The aberrant sensorimotor, cortico-striatal, and cortico-limbic integrity may collectively underlie neurobiological mechanisms of MPDs.
The Maghreb (north-west Africa) played an important role during the Palaeolithic and later in connecting the western Mediterranean from the Phoenician to Islamic periods. Yet, knowledge of its later prehistory is limited, particularly between c. 4000 and 1000 BC. Here, the authors present the first results of investigations at Oued Beht, Morocco, revealing a hitherto unknown farming society dated to c. 3400–2900 BC. This is currently the earliest and largest agricultural complex in Africa beyond the Nile corridor. Pottery and lithics, together with numerous pits, point to a community that brings the Maghreb into dialogue with contemporaneous wider western Mediterranean developments.
Aquatic ecosystems - lakes, ponds and streams - are hotspots of biodiversity in the cold and arid environment of Continental Antarctica. Environmental change is expected to increasingly alter Antarctic aquatic ecosystems and modify the physical characteristics and interactions within the habitats that they support. Here, we describe physical and biological features of the peripheral ‘moat’ of a closed-basin Antarctic lake. These moats mediate connectivity amongst streams, lake and soils. We highlight the cyclical moat transition from a frozen winter state to an active open-water summer system, through refreeze as winter returns. Summer melting begins at the lakebed, initially creating an ice-constrained lens of liquid water in November, which swiftly progresses upwards, creating open water in December. Conversely, freezing progresses slowly from the water surface downwards, with water at 1 m bottom depth remaining liquid until May. Moats support productive, diverse benthic communities that are taxonomically distinct from those under the adjacent permanent lake ice. We show how ion ratios suggest that summer exchange occurs amongst moats, streams, soils and sub-ice lake water, perhaps facilitated by within-moat density-driven convection. Moats occupy a small but dynamic area of lake habitat, are disproportionately affected by recent lake-level rises and may thus be particularly vulnerable to hydrological change.
This book introduces convex polytopes and their graphs, alongside the results and methodologies required to study them. It guides the reader from the basics to current research, presenting many open problems to facilitate the transition. The book includes results not previously found in other books, such as: the edge connectivity and linkedness of graphs of polytopes; the characterisation of their cycle space; the Minkowski decomposition of polytopes from the perspective of geometric graphs; Lei Xue's recent lower bound theorem on the number of faces of polytopes with a small number of vertices; and Gil Kalai's rigidity proof of the lower bound theorem for simplicial polytopes. This accessible introduction covers prerequisites from linear algebra, graph theory, and polytope theory. Each chapter concludes with exercises of varying difficulty, designed to help the reader engage with new concepts. These features make the book ideal for students and researchers new to the field.
This is the first volume on the history of the Nile Delta to cover the c.7000 years from the Predynastic period to the twentieth century. It offers a multidisciplinary approach engaging with varied aspects of the region's long, complex, yet still underappreciated history. Readers will learn of the history of settlement, agriculture and the management of water resources at different periods and in different places, as well as the naming and mapping of the Delta and the roles played by tourism and archaeology. The wide range of backgrounds of the contributors and the broad panoply of methodological and conceptual practices deployed enable new spaces to be opened up for conversations and cross-fertilization across disciplinary and chronological boundaries. The result is a potent tribute to the historical significance of this region and the instrumental role it has played in the shaping of past, present and future Afro-Eurasian worlds.